The Reagan administration has begun "winding down" intensified searches along the Mexican border that have caused long delays at entry points, but the administration is "not at all satisfied" with Mexico's cooperation in the case of a kidnaped U.S. Drug Enforcement Administration agent, officials said yesterday.

Reagan discussed the border searches and the abduction of Enrique Camarena Salazar by telephone yesterday with Mexican President Miguel de la Madrid, a White House official said. The 15-minute call was made by the Mexican president, the official said.

Reagan expressed concern for Camarena's safety and that of other Americans in Mexico, said the official, who declined to provide further details of the call.

Special correspondent William Orme reported from Mexico City last night that Reagan told de la Madrid that the United States will end its intensive searches of Mexican border traffic "in the shortest time possible," according to de la Madrid's press office.

The two also agreed in principle to have the U.S. and Mexican attorneys general meet to discuss bilateral drug-control efforts, the office said. De la Madrid is reported to have told Reagan that Mexican police "are making their best effort" to find Camarena.

De la Madrid told Reagan that "extreme" U.S. Customs Service measures were "seriously damaging the relationship between the two sides of the border" and were "not the most appropriate means of combating drug traffic," the office said.

Earlier, Reagan sent a personal letter to de la Madrid seeking better cooperation from his government in the kidnaping investigation, the officials said.

The administration is "kind of ticked off" that Mexican authorities have not given more cooperation, a second administration official said.

It was understood that U.S. officials are concerned that one Mexican police organization called to investigate the abduction may have been involved in it.

Last week, frustrated U.S. officials considered having Reagan personally telephone de la Madrid, but instead Reagan sent a letter last weekend while vacationing in Santa Barbara, Calif.

White House spokesman Larry Speakes said yesterday, "We would like to have more cooperation and the only tangible evidence of cooperation would be some progress in solving the case . . . . "

The stepped-up inspections provoked complaints of economic hardship in key border regions and an expression of "deep concern" delivered to Deputy Secretary of State Kenneth W. Dam from Mexican Ambassador Jorge Espinosa. Sen. Lloyd Bentsen (D-Tex.) said yesterday that he believed that the border inspections would be eased this weekend.

Sources said that U.S. Ambassador to Mexico John A. Gavin came to Washington this week with a recommendation that the intensified border searches be relaxed, as they have been in the last few days.

A Customs Service spokesman said yesterday that backups at the border, which lasted up to eight hours last weekend, were running an hour to 90 minutes yesterday.

The intensified searches "achieved their purpose," one senior official said, adding that the purpose was to get Mexico's "attention" focused on the kidnap case.

The public explanation of the car-by-car searches was that U.S. officials were seeking information about the abduction and trying to prevent those responsible from slipping into the United States.

But privately, officials said the inspections were ordered out of U.S. frustration that Mexico's help in the probe was not sufficient.

State Department spokesman Edward Djerejian said yesterday, "If any message was conveyed to the Mexican government by the border measures, it was that we are serious and determined about doing everything possible to obtain the safe return of our agent. Based on the conversations which have occurred within the last few days, I think the Mexican government shares our sense of urgency."

The State Department has expressed concern about six other Americans missing and believed kidnaped in Mexico.

Meanwhile, a group of congressmen who represent districts along the border demanded an end to the checkpoint inspections. Rep. Ronald Coleman, a Democrat from El Paso, said the backup at the border has "paralyzed" commerce. He said Congress has been given no evidence that the inspections have aided the search for Camarena.